     [repjob cfgjob]))
 
 
+#_(defmethod cmn/run-xcomparison :rnaseq
+  [_ eid recipient compfile get-toolinfo template]
+  (run-rnaseq-comparison
+   eid recipient compfile get-toolinfo template))
+
 (defmethod cmn/run-comparison :rnaseq
   [_ eid recipient compfile get-toolinfo template]
   (run-rnaseq-comparison

  (apply get-comparison-files- args))


(defn split-filter-fastqs
  [eid]
  (cmn/split-filter-fastqs eid identity))

;;; Get primary phase 1 arguments. These are the bowtie index, the
;;; fastq set, output bam and bai file names
(defmethod cmn/get-phase-1-args :rnaseq
  [_ eid repname & {:keys [repk star]}]
  (let [fqs (cljstr/join "," (cmn/get-replicate-fqzs eid repname repk))
        refnm (cmn/replicate-name->strain-name eid repname)
        btindex (fs/join (cmn/get-exp-info eid :index) refnm)
        starindex (when star
                    (fs/join (cmn/get-exp-info eid :starindex) refnm))
        starprefix (when star
                     (fs/join (cmn/get-exp-info eid repk :star) repname))
        otbam (fs/join (cmn/get-exp-info eid repk :bams) (str repname ".bam"))
        otbai (str otbam ".bai")
        refgtf (fs/join (cmn/get-exp-info eid :refs)
                        (str refnm ".gtf"))]
    (apply cmn/ensure-dirs (map fs/dirname [otbam otbai]))
    (when star (cmn/ensure-dirs (fs/dirname starprefix)))
    (if star
      [starindex fqs otbam otbai starprefix]
      [btindex fqs otbam otbai])))


(defn get-phase-2-dirs [eid repk]
